def test_explicit_ode_system(testdata):
model = Model(testdata / 'nonmem' / 'pheno.mod')
explicit_odes(model)
assert 'A_OUTPUT(0) = 0' in str(model.statements.ode_system)
assert model.statements.ode_system.rhs_symbols == {
S('t'), S('AMT'), S('CL'), S('V')
}
def test_ode_free_symbols(testdata):
model = Model(testdata / 'nonmem' / 'pheno_real.mod')
assert model.statements.ode_system.free_symbols == {S('V'), S('CL'), S('AMT'), S('t')}
explicit_odes(model)
odes = model.statements.ode_system
assert odes.free_symbols == {S('V'), S('CL'), S('AMT'), S('t')}
def force_des(model, odes):
"""Switch to $DES if necessary"""
if isinstance(odes, ExplicitODESystem):
return
amounts = {sympy.Function(amt.name)(symbol('t')) for amt in odes.amounts}
if odes.atoms(sympy.Function) & amounts:
modeling.explicit_odes(model)
new = model.statements.ode_system
to_des(model, new)
def force_des(model, odes):
"""Switch to $DES if necessary"""
if isinstance(odes, ExplicitODESystem):
return
# Import put here to avoid circular import in Python 3.6
import pharmpy.modeling as modeling
amounts = {sympy.Function(amt.name)(symbol('t')) for amt in odes.amounts}
if odes.atoms(sympy.Function) & amounts:
modeling.explicit_odes(model)
new = model.statements.ode_system
to_des(model, new)
def test_explicit_ode_system(testdata):
model = Model(testdata / 'nonmem' / 'pheno.mod')
explicit_odes(model)
assert 'A_OUTPUT(0) = 0' in str(model.statements.ode_system)
assert model.statements.ode_system.rhs_symbols == {S('t'), S('AMT'), S('CL'), S('V')}
odes = ExplicitODESystem([sympy.Eq(S('x'), S('y'))], {})
assert str(odes) == '{x = y'
assert odes._repr_latex_() == '\\begin{cases} \\displaystyle x = y \\end{cases}'
odes = ExplicitODESystem([sympy.Eq(S('x'), S('y')), sympy.Eq(S('z'), S('y'))], {})
assert 'x = y' in str(odes)
odes = ExplicitODESystem([sympy.Eq(S('x'), 1)], {})
assert odes.free_symbols == {S('x')}
def test_to_explicit_odes(pheno_path, testdata):
model = Model(pheno_path)
explicit_odes(model)
model.update_source()
lines = str(model).split('\n')
assert lines[5] == '$MODEL COMPARTMENT=(CENTRAL DEFDOSE)'
assert lines[16] == '$DES'
assert lines[17] == 'DADT(1) = -A(1)*CL/V'
model = Model(testdata / 'nonmem' / 'modeling' /
'pheno_advan1_zero_order.mod')
explicit_odes(model)
model.update_source()
lines = str(model).split('\n')
assert lines[15] == 'D1 = THETA(4)'
def test_explicit_odes(model):
explicit_odes(model)